Automated identification of flagella from videomicroscopy via the medial axis transform

Benjamin J. Walker, Kenta Ishimoto, Richard J. Wheeler

Research output: Contribution to journalArticlepeer-review

4 Citations (SciVal)


Ubiquitous in eukaryotic organisms, the flagellum is a well-studied organelle that is well-known to be responsible for motility in a variety of organisms. Commonly necessitated in their study is the capability to image and subsequently track the movement of one or more flagella using videomicroscopy, requiring digital isolation and location of the flagellum within a sequence of frames. Such a process in general currently requires some researcher input, providing some manual estimate or reliance on an experiment-specific heuristic to correctly identify and track the motion of a flagellum. Here we present a fully-automated method of flagellum identification from videomicroscopy based on the fact that the flagella are of approximately constant width when viewed by microscopy. We demonstrate the effectiveness of the algorithm by application to captured videomicroscopy of Leishmania mexicana, a parasitic monoflagellate of the family Trypanosomatidae. ImageJ Macros for flagellar identification are provided, and high accuracy and remarkable throughput are achieved via this unsupervised method, obtaining results comparable in quality to previous studies of closely-related species but achieved without the need for precursory measurements or the development of a specialised heuristic, enabling in general the automated generation of digitised kinematic descriptions of flagellar beating from videomicroscopy.

Original languageEnglish
Article number5015
JournalScientific Reports
Issue number1
Publication statusPublished - 21 Mar 2019

Bibliographical note

Funding Information:
B.J.W. is supported by the UK Engineering and Physical Sciences Research Council (EPSRC), grant EP/ N509711/1. K.I. is supported by JSPS Overseas Research Fellowship (29-0146), MEXT Leading Initiative for Excellent Young Researchers (LEADER), and JSPS KAKENHI Grant Number JP18K13456. R.J.W. is supported by the Wellcome Trust [103261/Z/13/Z,211075/Z/18/Z], with equipment supported by a Wellcome Trust Investigator Award [104627/Z/14/Z].

Publisher Copyright:
© 2019, The Author(s).

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Automated identification of flagella from videomicroscopy via the medial axis transform'. Together they form a unique fingerprint.

Cite this